Dear all,
Related to the bug that was reported in 2011 (see http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html) with the way that surface-based volumes and areas were calculated in Freesurfer versions 5.1 and earlier, I’d like to confirm that region-of-interest measures obtained using those earlier versions (e.g. when exporting the volume / surface area to tables using aparcstats2table) were unaffected by this bug (i.e. rerunning qcache should not change ROI-based results).
2. I’d like to also confirm that otherwise, for vertex-based analyses, it should be sufficient to run ‘recon-all subject –qcache’ using a more recent version of freesurfer in order to obtain accurate measures for data that was originally processed using 'recon-all –all' with an earlier version of freesurfer (I have data that was originally processed with version 4.4 and other data that was processed with version 5.1 that I would like to now examine in a surface-based manner).
3. The bug was related to how the measures were converted to standard space - I’d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
Many thanks, and all the best, Narly.
On 03/16/2014 06:07 PM, Narly Golestani wrote:
Dear all,
Related to the bug that was reported in 2011 (see http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg19821.html) with the way that surface-based volumes and areas were calculated in Freesurfer versions 5.1 and earlier, I’d like to confirm that region-of-interest measures obtained using those earlier versions (e.g. when exporting the volume / surface area to tables using aparcstats2table) were unaffected by this bug (i.e. rerunning qcache should not change ROI-based results).
Correct, the aparcstats2table values are unaffected.
- I’d like to also confirm that otherwise, for vertex-based analyses,
it should be sufficient to run ‘recon-all subject –qcache’ using a more recent version of freesurfer in order to obtain accurate measures for data that was originally processed using 'recon-all –all' with an earlier version of freesurfer (I have data that was originally processed with version 4.4 and other data that was processed with version 5.1 that I would like to now examine in a surface-based manner).
Yes, that works fine.
- The bug was related to how the measures were converted to standard
space - I’d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Many thanks, and all the best,
Narly.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to standard
space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
The vertex-based measures are computed in individual space, not standard space doug
On 03/17/2014 05:12 PM, Narly Golestani wrote:
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to standard
space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures?
Thanks, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
The vertex-based measures are computed in individual space, not standard space doug
On 03/17/2014 05:12 PM, Narly Golestani wrote:
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to standard
space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Sorry, the thread of the email that explains the problem and the fix are not included below. Can you re-explain? We get a lot of emails here and it is not possible to remember the context of each one. doug
On 03/18/2014 11:32 AM, _andreia_@sapo.pt wrote:
Hi all,
just two quick questions: to what FS version is this related? And what is wrong to do if one does not have the fix? Using what stats/procedures?
Thanks, Andreia
Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:
why would one control for total brain volume in doing vertex-based
analyses when the vertex-based measures are computed in standard space?
The vertex-based measures are computed in individual space, not standard space doug
On 03/17/2014 05:12 PM, Narly Golestani wrote:
Dear Doug,
Many thanks for your answers.
- The bug was related to how the measures were converted to standard
space - I?d like to therefore confirm that when doing surface/vertex-based analyses, it is not necessary to use total brain volume as a covariate (whereas it is for ROI-based analyses).
This question has nothing to do with the bug. People generally use ICV or total brain volume when exploring cortical volume or surface area, but it is inappropriate for thicknss studies doug
Regarding the last point (which indeed has nothing to do with the bug, sorry for having given the impression that I thought that it did), why would one control for total brain volume in doing vertex-based analyses when the vertex-based measures are computed in standard space? I realize that this has to be done for ROI analyses since these measures are in native space.
Thanks again, and best, Narly.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
_andreia_＠sapo.pt -
Douglas N Greve -
Narly Golestani